National Higher Education Fund Corporation (PTPTN) is an important agency that provides funding to the students who are qualified to further their studies at a higher level of institutions. As this agency dealing with financial assistance, the interaction between the agency and its customer is very high. This research focussed on the customer satisfaction on counter service quality at PTPTN and the relationship with their organizational performance focussing on client charter. The key elements of customer satisfaction are tangibility, reliability, responsiveness, assurance and empathy. There are four (4) research objectives for this research study constructed which is to study the level organizational performance of PTPTN in terms of their client charter achievement, level of customer satisfaction on counter service quality provided at PTPTN, identify whether customer satisfaction on counter service quality at PTPTN have a relationship with its organizational performance based on its client charter and also identify whether different customer‟s gender affect the organizational performance at PTPTN based on its client charter. A set of questionnaire was distributed to 381 individual respondents who are students from three universities at Klang Valley to represent the population for this study. This study utilized Likert-scale questions to answer both independent and dependent variables. The data collected were tested of its goodness of data via a series of tests and being analyzed using Statistical Package for the Social Sciences (SPSS) version 19.0. Analyses carried out revealed that, PTPTN are working toward achievement of their organizational performance stated in their client charter and students are satisfied with the counter service quality provided by PTPTN, however there is low and moderate relationship between dimension in customer satisfaction on counter service quality at PTPTN and their organizational performance based on their client charter. On the other, it also found that there are no significant differences between genders towards the organizational performance based on client charter in this study. Lastly, there are several recommendations suggested in this research for future improvement in service quality which is by increasing exposure about a client charter to the customer, improving their service tangibility and reliability and improving their complaint management.